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36 * Registers command-line modules for pre-5.0 binaries.
38 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 #include "legacymodules.h"
44 #include "gromacs/commandline/cmdlinemodule.h"
45 #include "gromacs/commandline/cmdlinemodulemanager.h"
47 #include "gromacs/gmxana/gmx_ana.h"
48 #include "gromacs/gmxpreprocess/grompp.h"
49 #include "gromacs/gmxpreprocess/pdb2gmx.h"
50 #include "gromacs/gmxpreprocess/protonate.h"
51 #include "gromacs/gmxpreprocess/x2top.h"
52 #include "gromacs/tools/check.h"
53 #include "gromacs/tools/dump.h"
54 #include "gromacs/tools/convert_tpr.h"
56 #include "mdrun/mdrun_main.h"
57 #include "view/view.h"
63 * Command line module that provides information about obsolescence.
65 * Prints a message directing the user to a wiki page describing replacement
68 class ObsoleteToolModule : public gmx::CommandLineModuleInterface
71 //! Creates an obsolete tool module for a tool with the given name.
72 explicit ObsoleteToolModule(const char *name)
77 virtual const char *name() const
81 virtual const char *shortDescription() const
86 virtual int run(int /*argc*/, char * /*argv*/[])
91 virtual void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const
97 void printMessage() const
100 "This tool has been removed from Gromacs 5.0. Please see\n"
101 " http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0\n"
102 "for ideas how to perform the same tasks with the "
111 * Convenience function for creating and registering a module.
113 * \param[in] manager Module manager to which to register the module.
114 * \param[in] mainFunction Main function to wrap.
115 * \param[in] name Name for the new module.
116 * \param[in] shortDescription One-line description for the new module.
118 void registerModule(gmx::CommandLineModuleManager *manager,
119 gmx::CommandLineModuleManager::CMainFunction mainFunction,
120 const char *name, const char *shortDescription)
122 manager->addModuleCMain(name, shortDescription, mainFunction);
126 * Convenience function for registering a module for an obsolete tool.
128 * \param[in] manager Module manager to which to register the module.
129 * \param[in] name Name for the obsolete tool.
131 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
134 gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
135 manager->addModule(move(module));
140 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
142 // Modules from this directory (were in src/kernel/).
143 registerModule(manager, &gmx_check, "check",
144 "Check and compare files");
145 registerModule(manager, &gmx_dump, "dump",
146 "Make binary files human readable");
147 registerModule(manager, &gmx_grompp, "grompp",
148 "Make a run input file");
149 registerModule(manager, &gmx_pdb2gmx, "pdb2gmx",
150 "Convert coordinate files to topology and FF-compliant coordinate files");
151 registerModule(manager, &gmx_convert_tpr, "convert-tpr",
152 "Make a modifed run-input file");
154 registerModule(manager, &gmx_protonate, "protonate",
155 "Protonate structures");
156 registerModule(manager, &gmx_x2top, "x2top",
157 "Generate a primitive topology from coordinates");
159 registerModule(manager, &gmx_mdrun, "mdrun",
160 "Perform a simulation, do a normal mode analysis or an energy minimization");
162 // Modules from gmx_ana.h.
163 registerModule(manager, &gmx_do_dssp, "do_dssp",
164 "Assign secondary structure and calculate solvent accessible surface area");
165 registerModule(manager, &gmx_editconf, "editconf",
166 "Convert and manipulates structure files");
167 registerModule(manager, &gmx_eneconv, "eneconv",
168 "Convert energy files");
169 registerModule(manager, &gmx_genbox, "genbox",
171 registerModule(manager, &gmx_genconf, "genconf",
172 "Multiply a conformation in 'random' orientations");
173 registerModule(manager, &gmx_genion, "genion",
174 "Generate monoatomic ions on energetically favorable positions");
175 registerModule(manager, &gmx_genpr, "genrestr",
176 "Generate position restraints or distance restraints for index groups");
177 registerModule(manager, &gmx_make_edi, "make_edi",
178 "Generate input files for essential dynamics sampling");
179 registerModule(manager, &gmx_make_ndx, "make_ndx",
181 registerModule(manager, &gmx_mk_angndx, "mk_angndx",
182 "Generate index files for 'gmx angle'");
183 registerModule(manager, &gmx_trjcat, "trjcat",
184 "Concatenate trajectory files");
185 registerModule(manager, &gmx_trjconv, "trjconv",
186 "Convert and manipulates trajectory files");
187 registerModule(manager, &gmx_trjorder, "trjorder",
188 "Order molecules according to their distance to a group");
189 registerModule(manager, &gmx_xpm2ps, "xpm2ps",
190 "Convert XPM (XPixelMap) matrices to postscript or XPM");
192 registerModule(manager, &gmx_anadock, "anadock",
193 "Cluster structures from Autodock runs");
194 registerModule(manager, &gmx_anaeig, "anaeig",
195 "Analyze eigenvectors/normal modes");
196 registerModule(manager, &gmx_analyze, "analyze",
197 "Analyze data sets");
198 registerModule(manager, &gmx_g_angle, "angle",
199 "Calculate distributions and correlations for angles and dihedrals");
200 registerModule(manager, &gmx_bar, "bar",
201 "Calculate free energy difference estimates through Bennett's acceptance ratio");
202 registerObsoleteTool(manager, "bond");
203 registerObsoleteTool(manager, "dist");
204 registerObsoleteTool(manager, "sgangle");
206 registerModule(manager, &gmx_bundle, "bundle",
207 "Analyze bundles of axes, e.g., helices");
208 registerModule(manager, &gmx_chi, "chi",
209 "Calculate everything you want to know about chi and other dihedrals");
210 registerModule(manager, &gmx_cluster, "cluster",
211 "Cluster structures");
212 registerModule(manager, &gmx_clustsize, "clustsize",
213 "Calculate size distributions of atomic clusters");
214 registerModule(manager, &gmx_confrms, "confrms",
215 "Fit two structures and calculates the RMSD");
216 registerModule(manager, &gmx_covar, "covar",
217 "Calculate and diagonalize the covariance matrix");
218 registerModule(manager, &gmx_current, "current",
219 "Calculate dielectric constants and current autocorrelation function");
220 registerModule(manager, &gmx_density, "density",
221 "Calculate the density of the system");
222 registerModule(manager, &gmx_densmap, "densmap",
223 "Calculate 2D planar or axial-radial density maps");
224 registerModule(manager, &gmx_densorder, "densorder",
225 "Calculate surface fluctuations");
226 registerModule(manager, &gmx_dielectric, "dielectric",
227 "Calculate frequency dependent dielectric constants");
228 registerModule(manager, &gmx_dipoles, "dipoles",
229 "Compute the total dipole plus fluctuations");
230 registerModule(manager, &gmx_disre, "disre",
231 "Analyze distance restraints");
232 registerModule(manager, &gmx_dos, "dos",
233 "Analyze density of states and properties based on that");
234 registerModule(manager, &gmx_dyecoupl, "dyecoupl",
235 "Extract dye dynamics from trajectories");
236 registerModule(manager, &gmx_dyndom, "dyndom",
237 "Interpolate and extrapolate structure rotations");
238 registerModule(manager, &gmx_enemat, "enemat",
239 "Extract an energy matrix from an energy file");
240 registerModule(manager, &gmx_energy, "energy",
241 "Writes energies to xvg files and display averages");
242 registerModule(manager, &gmx_filter, "filter",
243 "Frequency filter trajectories, useful for making smooth movies");
244 registerModule(manager, &gmx_gyrate, "gyrate",
245 "Calculate the radius of gyration");
246 registerModule(manager, &gmx_h2order, "h2order",
247 "Compute the orientation of water molecules");
248 registerModule(manager, &gmx_hbond, "hbond",
249 "Compute and analyze hydrogen bonds");
250 registerModule(manager, &gmx_helix, "helix",
251 "Calculate basic properties of alpha helices");
252 registerModule(manager, &gmx_helixorient, "helixorient",
253 "Calculate local pitch/bending/rotation/orientation inside helices");
254 registerModule(manager, &gmx_hydorder, "hydorder",
255 "Compute tetrahedrality parameters around a given atom");
256 registerModule(manager, &gmx_kinetics, "kinetics",
257 "Analyze kinetic constants from properties based on the Eyring model");
258 registerModule(manager, &gmx_lie, "lie",
259 "Estimate free energy from linear combinations");
260 registerModule(manager, &gmx_mdmat, "mdmat",
261 "Calculate residue contact maps");
262 registerModule(manager, &gmx_mindist, "mindist",
263 "Calculate the minimum distance between two groups");
264 registerModule(manager, &gmx_morph, "morph",
265 "Interpolate linearly between conformations");
266 registerModule(manager, &gmx_msd, "msd",
267 "Calculates mean square displacements");
268 registerModule(manager, &gmx_nmeig, "nmeig",
269 "Diagonalize the Hessian for normal mode analysis");
270 registerModule(manager, &gmx_nmens, "nmens",
271 "Generate an ensemble of structures from the normal modes");
272 registerModule(manager, &gmx_nmtraj, "nmtraj",
273 "Generate a virtual oscillating trajectory from an eigenvector");
274 registerModule(manager, &gmx_options, "options", NULL);
275 registerModule(manager, &gmx_order, "order",
276 "Compute the order parameter per atom for carbon tails");
277 registerModule(manager, &gmx_pme_error, "pme_error",
278 "Estimate the error of using PME with a given input file");
279 registerModule(manager, &gmx_polystat, "polystat",
280 "Calculate static properties of polymers");
281 registerModule(manager, &gmx_potential, "potential",
282 "Calculate the electrostatic potential across the box");
283 registerModule(manager, &gmx_principal, "principal",
284 "Calculate principal axes of inertia for a group of atoms");
285 registerModule(manager, &gmx_rama, "rama",
286 "Compute Ramachandran plots");
287 registerModule(manager, &gmx_rdf, "rdf",
288 "Calculate radial distribution functions");
289 registerModule(manager, &gmx_rms, "rms",
290 "Calculate RMSDs with a reference structure and RMSD matrices");
291 registerModule(manager, &gmx_rmsdist, "rmsdist",
292 "Calculate atom pair distances averaged with power -2, -3 or -6");
293 registerModule(manager, &gmx_rmsf, "rmsf",
294 "Calculate atomic fluctuations");
295 registerModule(manager, &gmx_rotacf, "rotacf",
296 "Calculate the rotational correlation function for molecules");
297 registerModule(manager, &gmx_rotmat, "rotmat",
298 "Plot the rotation matrix for fitting to a reference structure");
299 registerModule(manager, &gmx_saltbr, "saltbr",
300 "Compute salt bridges");
301 registerModule(manager, &gmx_sans, "sans",
302 "Compute small angle neutron scattering spectra");
303 registerModule(manager, &gmx_sas, "sas",
304 "Compute solvent accessible surface area");
305 registerModule(manager, &gmx_saxs, "saxs",
306 "Compute small angle X-ray scattering spectra");
307 registerModule(manager, &gmx_sham, "sham",
308 "Compute free energies or other histograms from histograms");
309 registerModule(manager, &gmx_sigeps, "sigeps",
310 "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
311 registerModule(manager, &gmx_sorient, "sorient",
312 "Analyze solvent orientation around solutes");
313 registerModule(manager, &gmx_spatial, "spatial",
314 "Calculate the spatial distribution function");
315 registerModule(manager, &gmx_spol, "spol",
316 "Analyze solvent dipole orientation and polarization around solutes");
317 registerModule(manager, &gmx_tcaf, "tcaf",
318 "Calculate viscosities of liquids");
319 registerModule(manager, &gmx_traj, "traj",
320 "Plot x, v, f, box, temperature and rotational energy from trajectories");
321 registerModule(manager, &gmx_tune_pme, "tune_pme",
322 "Time mdrun as a function of PME nodes to optimize settings");
323 registerModule(manager, &gmx_vanhove, "vanhove",
324 "Compute Van Hove displacement and correlation functions");
325 registerModule(manager, &gmx_velacc, "velacc",
326 "Calculate velocity autocorrelation functions");
327 registerModule(manager, &gmx_wham, "wham",
328 "Perform weighted histogram analysis after umbrella sampling");
329 registerModule(manager, &gmx_wheel, "wheel",
330 "Plot helical wheels");
331 registerModule(manager, &gmx_view, "view",
332 "View a trajectory on an X-Windows terminal");
335 gmx::CommandLineModuleGroup group =
336 manager->addModuleGroup("Generating topologies and coordinates");
337 group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
338 group.addModule("protonate");
339 group.addModule("x2top");
340 group.addModule("genbox");
341 group.addModule("genconf");
342 group.addModule("genion");
343 group.addModule("genrestr");
344 group.addModule("pdb2gmx");
347 gmx::CommandLineModuleGroup group =
348 manager->addModuleGroup("Running a simulation");
349 group.addModule("grompp");
350 group.addModule("mdrun");
351 group.addModule("convert-tpr");
354 gmx::CommandLineModuleGroup group =
355 manager->addModuleGroup("Viewing trajectories");
356 group.addModule("nmtraj");
357 group.addModule("view");
360 gmx::CommandLineModuleGroup group =
361 manager->addModuleGroup("Processing energies");
362 group.addModule("enemat");
363 group.addModule("energy");
364 group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
367 gmx::CommandLineModuleGroup group =
368 manager->addModuleGroup("Converting files");
369 group.addModule("editconf");
370 group.addModule("eneconv");
371 group.addModule("sigeps");
372 group.addModule("trjcat");
373 group.addModule("trjconv");
374 group.addModule("xpm2ps");
377 gmx::CommandLineModuleGroup group =
378 manager->addModuleGroup("Tools");
379 group.addModule("analyze");
380 group.addModule("dyndom");
381 group.addModule("filter");
382 group.addModule("lie");
383 group.addModule("morph");
384 group.addModule("pme_error");
385 group.addModule("sham");
386 group.addModule("spatial");
387 group.addModule("traj");
388 group.addModule("tune_pme");
389 group.addModule("wham");
390 group.addModule("check");
391 group.addModule("dump");
392 group.addModule("make_ndx");
393 group.addModule("mk_angndx");
394 group.addModule("trjorder");
395 group.addModule("xpm2ps");
398 gmx::CommandLineModuleGroup group =
399 manager->addModuleGroup("Distances between structures");
400 group.addModule("cluster");
401 group.addModule("confrms");
402 group.addModule("rms");
403 group.addModule("rmsf");
406 gmx::CommandLineModuleGroup group =
407 manager->addModuleGroup("Distances in structures over time");
408 group.addModule("mindist");
409 group.addModule("mdmat");
410 group.addModule("polystat");
411 group.addModule("rmsdist");
414 gmx::CommandLineModuleGroup group =
415 manager->addModuleGroup("Mass distribution properties over time");
416 group.addModule("gyrate");
417 group.addModule("msd");
418 group.addModule("polystat");
419 group.addModule("rdf");
420 group.addModule("rotacf");
421 group.addModule("rotmat");
422 group.addModule("sans");
423 group.addModule("saxs");
424 group.addModule("traj");
425 group.addModule("vanhove");
428 gmx::CommandLineModuleGroup group =
429 manager->addModuleGroup("Analyzing bonded interactions");
430 group.addModule("angle");
431 group.addModule("mk_angndx");
434 gmx::CommandLineModuleGroup group =
435 manager->addModuleGroup("Structural properties");
436 group.addModule("anadock");
437 group.addModule("bundle");
438 group.addModule("clustsize");
439 group.addModule("disre");
440 group.addModule("hbond");
441 group.addModule("order");
442 group.addModule("principal");
443 group.addModule("rdf");
444 group.addModule("saltbr");
445 group.addModule("sas");
446 group.addModule("sorient");
447 group.addModule("spol");
450 gmx::CommandLineModuleGroup group =
451 manager->addModuleGroup("Kinetic properties");
452 group.addModule("bar");
453 group.addModule("current");
454 group.addModule("dos");
455 group.addModule("dyecoupl");
456 group.addModule("kinetics");
457 group.addModule("principal");
458 group.addModule("tcaf");
459 group.addModule("traj");
460 group.addModule("vanhove");
461 group.addModule("velacc");
464 gmx::CommandLineModuleGroup group =
465 manager->addModuleGroup("Electrostatic properties");
466 group.addModule("current");
467 group.addModule("dielectric");
468 group.addModule("dipoles");
469 group.addModule("potential");
470 group.addModule("spol");
471 group.addModule("genion");
474 gmx::CommandLineModuleGroup group =
475 manager->addModuleGroup("Protein-specific analysis");
476 group.addModule("do_dssp");
477 group.addModule("chi");
478 group.addModule("helix");
479 group.addModule("helixorient");
480 group.addModule("rama");
481 group.addModule("wheel");
484 gmx::CommandLineModuleGroup group =
485 manager->addModuleGroup("Interfaces");
486 group.addModule("bundle");
487 group.addModule("density");
488 group.addModule("densmap");
489 group.addModule("densorder");
490 group.addModule("h2order");
491 group.addModule("hydorder");
492 group.addModule("order");
493 group.addModule("potential");
496 gmx::CommandLineModuleGroup group =
497 manager->addModuleGroup("Covariance analysis");
498 group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
499 group.addModule("covar");
500 group.addModule("make_edi");
503 gmx::CommandLineModuleGroup group =
504 manager->addModuleGroup("Normal modes");
505 group.addModuleWithDescription("anaeig", "Analyze the normal modes");
506 group.addModule("nmeig");
507 group.addModule("nmtraj");
508 group.addModule("nmens");
509 group.addModule("grompp");
510 group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");